Our own data on the effects of probiotics and phytopreparations proteins recognizing glycoconjugates on representatives (bacteria and fungi) of conditionally pathogenic microbiocenoses of mucosal biotopes of open cavities of the human body are summarized. Such proteins act in biotope microbiocenosis with probiotic-like and conditionally pathogenic compartments as effective synergistic antibiotic-like antimicrobial agents, and target microbiocenoses are opposed as communicative bodies. The results indicate a wide range of antimicrobial agents of probiotics and phytopreparations, including lectins, enzymes of carbohydrate metabolism and exopolymer compounds (biosurfactants and others). The variety of probiotic and phytopreparation proteins that recognize and bind glycoconjugates is an important reserve for enhancing antimicrobial anti-pathogenic effects in the human body. Consideration of the role of such proteins in the body opens up new perspectives in the fight against microbial and viral pathogens in prophylaxis and therapy of human diseases.